Analysis of the algorithm: From rankings to backup genes.
Ranking section
Table 1. Performance summary for every kernel and net before integration.
| Net | Kernel | tpr_down_ci_0.95 | tpr_up_ci_0.95 | fpr_down_ci_0.95 | fpr_up_ci_0.95 | f |
|---|---|---|---|---|---|---|
| biological_process | ct | 1 | 1 | 1 | 1 | 0.904761904761905 |
| biological_process | el | 1 | 1 | 1 | 1 | 0.904761904761905 |
| biological_process | ka | 1 | 1 | 1 | 1 | 0.904761904761905 |
| biological_process | rf | 1 | 1 | 1 | 1 | 0.904761904761905 |
| cellular_component | ct | 1 | 1 | 1 | 1 | 0.90625 |
| cellular_component | el | 1 | 1 | 1 | 1 | 0.90625 |
| cellular_component | ka | 1 | 1 | 1 | 1 | 0.90625 |
| cellular_component | rf | 1 | 1 | 1 | 1 | 0.90625 |
| disease | ct | 0.5 | 1 | 0 | 1 | 0.956521739130435 |
| disease | el | 1 | 1 | 0.666666666666667 | 1 | 0.936170212765957 |
| disease | ka | 1 | 1 | 0.333333333333333 | 1 | 0.936170212765957 |
| disease | rf | 1 | 1 | 1 | 1 | 0.936170212765957 |
| gene_TF | el | 1 | 1 | 0 | 0 | 1 |
| gene_TF | ka | 1 | 1 | 1 | 1 | 0.5 |
| gene_TF | rf | 1 | 1 | 0 | 0 | 1 |
| gene_hgncGroup | el | 1 | 1 | 1 | 1 | 0.9 |
| gene_hgncGroup | ka | 1 | 1 | 1 | 1 | 0.9 |
| gene_hgncGroup | rf | 1 | 1 | 1 | 1 | 0.9 |
| genetic_interaction_effect_bicor | ct | 1 | 1 | 1 | 1 | 0.896551724137931 |
| genetic_interaction_effect_bicor | el | 1 | 1 | 1 | 1 | 0.896551724137931 |
| genetic_interaction_effect_bicor | ka | 1 | 1 | 1 | 1 | 0.896551724137931 |
| genetic_interaction_effect_bicor | rf | 1 | 1 | 1 | 1 | 0.896551724137931 |
| molecular_function | ct | 1 | 1 | 1 | 1 | 0.90625 |
| molecular_function | el | 1 | 1 | 1 | 1 | 0.90625 |
| molecular_function | ka | 1 | 1 | 1 | 1 | 0.90625 |
| molecular_function | rf | 0.620689655172414 | 1 | 0.5 | 1 | 0.919354838709677 |
| pathway | el | 1 | 1 | 0.5 | 1 | 0.91304347826087 |
| pathway | ka | 1 | 1 | 1 | 1 | 0.91304347826087 |
| pathway | rf | 0.0952380952380952 | 1 | 0.25 | 1 | 0.933333333333333 |
| phenotype | ct | 0.826086956521739 | 1 | 0.333333333333333 | 1 | 0.901960784313726 |
| phenotype | el | 0.347826086956522 | 1 | 0 | 0.666666666666667 | 0.958333333333333 |
| phenotype | ka | 1 | 1 | 0.5 | 1 | 0.884615384615384 |
| phenotype | rf | 0.65108695652174 | 1 | 0 | 0.666666666666667 | 0.958333333333333 |
| protein_interaction | el | 1 | 1 | 0.75 | 1 | 0.909090909090909 |
| protein_interaction | ka | 1 | 1 | 1 | 1 | 0.909090909090909 |
| protein_interaction | rf | 0.882916666666667 | 1 | 0.666666666666667 | 1 | 0.916030534351145 |
Table 2. Performance summary for every kernel after integration
| Integration | Kernel | tpr_down_ci_0.95 | tpr_up_ci_0.95 | fpr_down_ci_0.95 | fpr_up_ci_0.95 | f |
|---|---|---|---|---|---|---|
| integration_mean_by_presence | ct | 0.413362068965518 | 1 | 0.583333333333333 | 1 | 0.910569105691057 |
| integration_mean_by_presence | el | 1 | 1 | 0.75 | 1 | 0.909090909090909 |
| integration_mean_by_presence | ka | 1 | 1 | 1 | 1 | 0.909090909090909 |
| integration_mean_by_presence | rf | 1 | 1 | 0.75 | 1 | 0.909090909090909 |
| mean | ct | 0.379310344827586 | 1 | 0.583333333333333 | 1 | 0.910569105691057 |
| mean | el | 1 | 1 | 1 | 1 | 0.909090909090909 |
| mean | ka | 1 | 1 | 1 | 1 | 0.909090909090909 |
| mean | rf | 1 | 1 | 1 | 1 | 0.909090909090909 |
Backup Pairs Coverage By Layer Non integrated
Backup Pairs Coverage By Layer Integrated
Distribution of ranks in dataset by non integrated kernels
Distribution of ranks in dataset by Integrated kernels
ROC-AUCs for Non-integrated kernel and layer
ROC-AUCS for integrated kernels
CDF plots of non integrated kernels
ROC plots of non integrated kernels
ROC plots of integrated kernels
CDF plots of integrated kernels